Mass spectrometry-based proteomic analysis of complex biological samples
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Proteomics seeks to determine protein structure, modifications, localization, and protein-protein interactions in addition to protein expression levels. Although proteomics is often a large-scale endeavor on a global system, much of its attraction lies in the ability to focus its tools on selected populations of proteins in specific circumstances, contributing directly to address questions involving functions and mechanisms. With the advancement of analytical technology, mass spectrometry, which is capable of sequencing peptides/proteins and characterizing post-translational modifications (PTMs) in molecular details, has become the main power in proteomics. Furthermore, strategies developed to characterize individual proteins are now systematically applied to protein populations. To date, mass spectrometry has been used to map the complete primary structure of individual proteins, and is becoming a general method for the characterization of modified subproteomes in large-scale research. Through the work outlined in this dissertation, we first explored the applications of mass spectrometry on human embryonic stem cells and discovered over 3000 proteins and 500 PTMs; later, a quantitative glycoproteomic study was performed on human pancreatic ductal fluids and revealed several potential protein biomarkers for the early diagnosis of pancreatic cancer; finally, we developed and tested an HCD/ETD MS scheme for the site mapping of O-GlcNAc proteins, and further investigated the potential of its applicability to other types of protein PTM.